Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA.
J Chem Inf Model. 2013 Feb 25;53(2):452-60. doi: 10.1021/ci300506y. Epub 2013 Jan 31.
Human arginase is a binuclear manganese metalloenzyme that participates in the urea cycle. Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea and is linked to several disorders such as asthma and cancer. Currently, the protonation and tautomerization state of the substrate when bound to the active site, which contains two manganese ions, is not known. Knowledge of the charge-dependent behavior of arginine in the arginase I environment would be of utility toward understanding the catalytic mechanism and designing inhibitors of this enzyme. The arginine(+/0) species, including all possible neutral tautomers, were modeled using an aminoimidazole analog as template. All-atom molecular dynamics simulations were then performed on each of the charged and neutral species. In addition, a hydroxide ion was included in selected simulations to test its importance. Results show that the positively charged state of arginine is stable in the active site of arginase I, with that stabilization facilitated by the presence of hydroxide. Glu277 is indicated to play a role in stabilizing arginine in the active site and facilitating its ability to assume a catalytically competent conformation in the presence of hydroxide. The reported interactions and modeled arginine-bound arginase I structures can be used as a tool for structure-based inhibitor design, as experimental data on the structure of the substrate-enzyme complex is lacking.
人精氨酸酶是一种双核锰金属酶，参与尿素循环。精氨酸酶催化 L-精氨酸水解为 L-鸟氨酸和尿素，并与哮喘和癌症等几种疾病有关。目前，与包含两个锰离子的活性位点结合的底物的质子化和互变异构状态尚不清楚。了解精氨酸酶 I 环境中精氨酸的电荷依赖性行为对于理解催化机制和设计该酶的抑制剂将是有用的。使用氨基咪唑类似物作为模板对精氨酸(+/0)物种，包括所有可能的中性互变异构体进行建模。然后对每个带电和中性物种进行全原子分子动力学模拟。此外，在选定的模拟中还包括了一个氢氧根离子，以测试其重要性。结果表明，带正电荷的精氨酸在精氨酸酶 I 的活性部位稳定存在，氢氧根的存在促进了其稳定。Glu277 被表明在稳定精氨酸在活性部位和促进其在氢氧根存在下能够假设催化活性构象方面发挥作用。所报道的相互作用和模拟的精氨酸结合的精氨酸酶 I 结构可作为基于结构的抑制剂设计的工具，因为缺乏关于底物-酶复合物结构的实验数据。
